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Name:
Dr. Saumya Ray Chaudhuri
Expertise:
Molecular Microbiology, Cell Biology, Biochemistry, Gene therapy

Contact Address:

saumya@imtech.res.in; saumya@rocketmail.com; 09417727654.

Write-up of research and development interests/focus, past and present goals:

My research experience includes working in the field of molecular microbiology, cell biology and biochemistry. Upon completion my doctoral training in the year of 1997, I joined as a post-doc under the supervision of Late Prof. James Ofengand at the University of Miami, FL. The major focus of the lab was centered on the role and biogenesis of pseudouridine, a 5’ribosyl isomer of uridine present mostly in rRNA, tRNA and small nuclear and nucleolar RNA. During this period I gained experience in biochemistry, molecular as well as in microbiology by doing pseudouridine sequencing, assigning gene function of unknown ORF, gene disruption and rescuing the mutant phenotype. Our data documented that lack of function of certain pseudouridine synsthases exerts profound effect on bacterial physiology. Part of this study was published in RNA and J.Biol.Chem. From Miami I moved to Houston to gain knowledge in the field of cancer cell biology and gene therapy. I joined Dr. Richard L Hurwitz’s group in Texas childrens’ hospital, Baylor college of Medicine. There we established the role of hyaluronic acid in Adenoviral mediated transgene expression. This work was published in Molecular Therapy. At that time, the group was also studying the therapeutic delivery of photoreceptor proteins to diseased animals. The use of a viral vector to deliver the ABC4A protein, a member of the ABCR transporter family and a protein responsible for retinal transport was being explored. This protein is defective in juvenile macular degeneration (Stargardt’s Disease). I cloned the ABCR cDNA into a retroviral vector. Before I could do further, I got an offer from Institute of Microbial Technology to join as a scientist C.  I accepted this offer to start my independent career and joined this institute back in 2001.

Presently my lab focuses on the quorum sensing signal transduction of non-O1, non-O139 strains of V. cholerae.  Quorum sensing signal network controls a plethora of disparate cellular events including biofilm development and pathogenesis in this bacterium.  V. cholerae comprises of 220 serogroup.  We have chosen non-O1, non-O139 strains as they are diverse from their O1 and O139 counterparts.  The quorum sensing sensory network of V. cholerae O1 reveals a complex architecture where collaboration among myriad of factors are required to stimulate the expression of a cascade of small RNA to control a range of events.  This regulation is tightly controlled by cell density. We have embarked on a project to understand the interplay between various regulatory molecules of this sensory network in non-O1, non-O139 strains of V. cholerae.  Thus far, several strains of diverse serogroup have been identified which harbor defect in the regulatory proteins and give rise to altered phenotype (Raychaudhuri et al., 2006; Dongre et al., 2008, Dongre et al., 2011, Dongre et al., 2011, Singh et al., 2013; Singh et al, 2014).  We are in the process of understanding these defects in more detail manner.  Besides, we are also involved in deciphering the outcome of host- pathogen interaction through amoeba-bacteria model system. Initially, we worked with E. histolytica as a host (Jain et al., 2006).  Currently, we use Acanthamoeba as a model system as it exists in similar ecological niches as Vibrio does. This work is in collaboration with Prof. Gunnar Sandstrom, Sweden (Abd et al., 2010).  We have also selected budding yeast to explore the function of unique pathogenic determinants harboring eukaryotic domains.  We observed that ectopic expression of type III effector protein of Vibrio cholerae induces toxicity in the budding yeast (Tripathi et al., 2010; Tripathi et al., 2013; Bankapalli et al., 2015).  In addition, we are also exploring the functionality of effector proteins from other Vibrio species by employing budding yeast model system.  Taken together, we have initiated studies to understand the biology of Vibrio in the context of their pathogenesis and survival in diverse environmental conditions (Khatri et al., 2012; Khatri et al., 2013). In addition, we have taken a keen interest to understand the biology of mammalian gut-associated E. coli and how cross feeding of glucose metabolic products of gut associated E. coli and probiotic E. coli strains stymie the growth of Vibrio cholerae (Dureja et al., 2014, Sengupta et. al., 2017).

Selected list of Publications and Patents:

Saumya Raychaudhuri
PhD (1991-1997): Dr. Ranajit K Ghosh, Indian Institute of Chemical Biology, CSIR
Post doctoral experiences (1997-2000):
1)    Late Prof. Edward James (Jim) Ofengand (1997-1999): Biogenesis of Pseudouridine
2)    Dr. Richard (Rich) L Hurwitz (1999-2000): Ocular Gene Therapy, Retinoblastoma, Stargardt’s disease

Biogenesis of Pseudouridine and Ribosomology: An Escherichia coli perspective

The project was primarily focused on the functional characterization of different family of pseudouridine synthases in Escherichia coli.
 
Ref no: 2, 3 and 4

Ocular Gene therapy, Adenoviral transduction and involvement of CD44

This project is translational in nature, where gene therapy is taken into account of ameliorating progression of retinoblastoma. We have also tried to correct ocular genetic disorders by providing the correct gene through lenti-viral gene delivery system.
 
Ref no: 9

Biology of Vibrio cholerae and related Vibrios: emergence of multidrug resistant strains, quorum sensing regulatory  small RNAs, master regulators and natural variants, metabolic fitness

One of our main goals is to understand quorum sensing a “cell to cell” communication process by employing Vibrio cholerae as a model organism; gain further molecular insight into various components of such intricate cellular networking process by analyzing natural variants. In case of metabolic fitness, we have discovered the existence of ethanolamine utilization machinery in Vibrio species. Presently, we are investigating the significance of such metabolic pathway in the survival and virulence of such Vibrio strains.

Ref no: 5, 6, 7, 8, 10, 13, 14, 15, 18, 19 and 20

Type III effector molecules, WH2 domain proteins and model systems: Gaining functional insight of bacterial proteins exploiting model organisms

In this project, our aim is to develop yeast as a model system to study bacterial effector proteins deliver through T3SS.

Ref no: 12, 17 and 22

Bacterial ecology, cross domain cross talk:

Ref no: 8 and 11

Biology of Commensal E. coli and other intestinal pathogens

Ref no: 16, 21

Publications year wise:

1.    Pajni S, Sharma C, Basing N, Ghosh A, Ramamurthy T, Nair GB, Ramajayam S, Das B, Kar S, Roychowdhury S, et al. Studies on the genesis of Vibrio cholerae O139: Identification of probable progenitor strains.  J Med Microbiol. 1995 Jan; 42(1): 20-5.

2.    Raychaudhuri S, Conrad J, Hall BG, Ofengand J.  A pseudouridine synthase required for the formation of two universally conserved pseudouridines in ribosomal RNA is essential for normal growth of Escherichia coli.  RNA. 1998 Nov; 4(11): 1407-17.

3.    Raychaudhuri S, Niu L, Conrad J, Lane BG, Ofengand J. Functional effect of deletion and mutation of the Escherichia coli ribosomal RNA and tRNA pseudouridine synthase  RluA.  J Biol Chem. 1999 Jul; 274(27): 18880-6.

4.    Gutgsell NS, Del Campo MD, Raychaudhuri S, Ofengand J. A second function for pseudouridine synthases: A point mutant of RluD unable to form pseudouridines 1911, 1915, and    1917 in Escherichia coli 23S ribosomal RNA restores normal growth to an RluD-minus strain.  RNA. 2001 Jul; 7(7): 990-8.

5.    M.Thungapathra, Amita, Kislay K.Sinha, Saumya Ray Chaudhuri, Pallavi Garg, T.Ramamurthy, G.B.Nair and Amit Ghosh: Occurrence of Antiobiotic Resistance Gene Cassettes aac (6')-Ib, dfrA5, dfrA12, and ere A2 in Class I Integrons in Non 01, Non-0139 Vibrio cholerae Strains in India. Antimicrobial Agents and Chemotherapy, 2002, Sept; 46(9): 2948-2955.

6.    Amita, S Roy Chowdhury, M.Thungapathra, T. Ramamurthy, G.Balakrish Nair and Amit Ghosh: Class I Integrons and SXT elements in El Tor strains Isolated before and after 1992 Vibrio cholerae 0139 Outbreak, Calcutta, India. Emerging Infectious Diseases. 2003 April: 9 (4): 500-502.

7.    Saumya Raychaudhuri, Vibhu Jain and Mitesh Dongre: Identification of a constitutively active variant of LuxO that affects production of HA/protease and biofilm development in a non-O1, non- O139 Vibrio cholerae O110. Gene, 2006 Mar 15; 369:126-33.

8.    Vibhu Jain, Mitesh Dongre and Saumya Raychaudhuri: Interaction of Vibrio cholerae O139 with an intestinal parasite Entameoba histolytica. J Med Microbiol, 2006 Dec ; 55: 1755-6.

9.    Saumya Ray Chaudhuri, Joshua N Mallam, Patricia Chévez-Barrios, Lalita  Wadhwa1,Philip Ng, Mary Y. Hurwitz, and Richard L. Hurwitz: Modulation of Adenoviral Transduction In Vitro and In Vivo by Hyaluronan and its receptor CD44. Molecular Therapy 2007 Mar;15(3):566-70.

10.    Mitesh Dongre, Ranjana Tripathy, Vibhu Jain and Saumya Raychaudhuri: Functional independence of a variant LuxOPL91 from a non-O1, non-O139 V. cholerae over the activity of CsrA and Fis. J Med Microbiol 2008, 57: 1041-1045.

11.    Hadi Abd, Soni Priya Valeru, Susan Marouf Sami, Amir Saeed, Saumya Raychaudhuri, Gunnar Sandström.  Interaction between Vibrio mimicus and Acanthamoeba castellanii. Environ Microbiol Rep. 2010  2(1):166-171.

12.    Ranjana Tripathi, Chetna Dureja, Swati Haldar, Alok K Mondal, and Saumya Raychaudhuri.  VopF, a type III effector protein from a non-O1, non-O139 V. cholerae strain demonstrates toxicity in Saccharomyces cerevisiae model. J Med Microbiol 2010 ; 59(Pt 1):17-24.

13.    Dongre M, Khatri N, Dureja C, Raychaudhuri S. Alanine-scanning mutagenesis of selected residues in the N-terminal region alters the functionality of LuxO: lessons from a natural variant LuxOPL91. J Med Microbiol. 2011 Jun; 60(Pt 6):856-60.

14.    Dongre M, Singh NS, Dureja C, Pedda N, Solanki AK, Ashish , Raychaudhuri S. Evidence on how a conserved glycine in the hinge region of HapR regulates its DNA binding ability: lessons from a natural variant. J Biol Chem. 2011 Apr 29; 286 (17):15043-9.

15.    Khatri N, Khatri I, Subramanian S, Raychaudhuri S. Ethanolamine utilization in Vibrio alginolyticus. Biol Direct. 2012 Dec 12; 7 (1):45. [Epub ahead of print]

16.    Indu Khatri, Chetna Dureja, Saumya Raychaudhuri, and Srikrishna Subramanian. Draft Genome Sequence of the Opportunistic Human Pathogen Morganella morganii SC01. Genome Announc. January 2013 1:e00051-12; doi:10.1128/genomeA.00051-12  http://genomea.asm.org/content/1/1/e00051-12.abstract.html?etoc

17.    Tripathi R, Kaithwas V, Dureja C, Raychaudhuri S. Alanine-scanning mutagenesis of WH2 domains of VopF reveals residues important for conferring lethality in a Saccharomyces cerevisiae model. Gene. 2013 Aug 1; 525(1):116-23. doi: 10.1016/j.gene.2013.04.071. Epub 2013 May 13.

18.    Khatri I, Mahajan S, Dureja C, Subramanian S, Raychaudhuri S. Evidence of a new metabolic capacity in an emerging diarrheal pathogen: lessons from the draft genomes of Vibrio fluvialis strains PG41 and I21563. Gut Pathog. 2013 Jul 29; 5 (1):20. [Epub ahead of print]

19.    Singh R, Rathore YS, Singh NS, Peddada N, Ashish, Raychaudhuri S. Substitution of Glutamate Residue by Lysine in the Dimerization Domain Affects DNA Binding Ability of HapR by Inducing Structural Deformity in the DNA Binding Domain. PLoS One. 2013 Oct 14;8(10):e76033. doi: 10.1371/journal.pone.0076033.

20.    Naorem Santa Singh, Sangita Kachhap, Richa Singh, Rahul Chandra Mishra, Balvinder Singh , Saumya Raychaudhuri.The length of glycine rich linker in DNA binding domain is critical for optimal functioning of quorum sensing master regulatory protein HapR. Mol Genet Genomics. 2014 Dec;289(6):1171-82. doi: 10.1007/s00438-014-0878-5. Epub 2014 Jul 5.

21.    Dureja C, Mahajan S, Raychaudhuri S. Phylogenetic Distribution and Prevalence of Genes Encoding Class I Integrons and CTX-M-15 Extended-Spectrum β-Lactamases in Escherichia coli Isolates from Healthy Humans in Chandigarh, India. PLoS One. 2014 Nov 19;9(11):e112551. doi: 10.1371/journal.pone.0112551. eCollection 2014.
 
22. Bankapalli LK, Mishra RC, Singh B, Raychaudhuri S. Identification of Critical Amino Acids Conferring Lethality in VopK, a Type III Effector Protein of Vibrio cholerae: Lessons from Yeast Model System. PLoS One. 2015 Oct 21; 10(10):e0141038. doi: 10.1371/journal.pone.0141038. eCollection 2015.
 
23. Gahlawat G, Shikha S, Chaddha BS, Chaudhuri SR, Mayilraj S, Choudhury AR. Microbial glycolipoprotein-capped silver nanoparticles as emerging antibacterial agents against cholera. Microb Cell Fact. 2016 Feb 1;15(1):25. doi: 10.1186/s12934-016-0422-x.
 
24.   Sengupta C, Ekka M, Arora S, Dhaware PD, Chowdhury R, Raychaudhuri S.Cross feeding of glucose metabolism byproducts of Escherichia coli human gut isolates and probiotic strains affect survival of Vibrio cholerae. Gut Pathog. 2017 Jan 17;9:3. doi: 10.1186/s13099-016-0153-x. eCollection 2017.
 
 
 
Patent Filed: 
 


  1. U.S. Patent entitled "HYALURONIC ACID MEDIATED ADENOVIRAL TRANSDUCTION" --- Saumya Ray Chaudhuri et al. Publication number: EP1480656 A4; PCT number: PCT/US2003/004571


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